# HG changeset patch
# User sanbi-uwc
# Date 1551688137 18000
# Node ID eaf51f9aff1072f6984dbfa9a95490fbb631009c
# Parent  53a61865e86e4a819b0efdcc788b1d60ed722dfe
planemo upload for repository https://github.com/COMBAT-TB/confil commit 9e5284a2616de5d869319f9c4436716a3f6656f8-dirty

diff -r 53a61865e86e -r eaf51f9aff10 confil.egg-info/PKG-INFO
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confil.egg-info/PKG-INFO	Mon Mar 04 03:28:57 2019 -0500
@@ -0,0 +1,38 @@
+Metadata-Version: 1.0
+Name: confil
+Version: 0.1.2.dev20190304
+Summary: Contamination filter
+Home-page: https://github.com/COMBAT-TB/confil
+Author: UNKNOWN
+Author-email: UNKNOWN
+License: UNKNOWN
+Description-Content-Type: text/markdown
+Description: # confil
+        
+        [![Build Status](https://travis-ci.org/COMBAT-TB/confil.svg?branch=master)](https://travis-ci.org/COMBAT-TB/confil)
+        [![Anaconda-Server Badge](https://anaconda.org/thoba/confil/badges/version.svg)](https://anaconda.org/thoba/confil)
+        
+        :no_entry_sign: :construction: **For in-house use**
+        
+        `confil` parses a [kraken2](https://ccb.jhu.edu/software/kraken2/) report and determines contamination based on a specified cutoff.
+        
+        ## Requirements
+        
+        - kraken2
+        
+        ## Up and running
+        
+        ```sh
+        $ git clone https://github.com/COMBAT-TB/confil.git
+        ...
+        $ cd confil
+        $ virtualenv envname
+        $ source envname/bin/activate
+        $ pip install -r requirements.txt
+        $ python setup.py install
+        $ confil --help
+        $ confil --threads 1 --paired --cutoff 80 fastq_1.fastq fastq_2.fastq
+        ```
+        
+Keywords: contamination,filter
+Platform: UNKNOWN
diff -r 53a61865e86e -r eaf51f9aff10 confil.egg-info/SOURCES.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confil.egg-info/SOURCES.txt	Mon Mar 04 03:28:57 2019 -0500
@@ -0,0 +1,15 @@
+README.md
+setup.cfg
+setup.py
+confil/__init__.py
+confil/confil.py
+confil/kraken.py
+confil/report.py
+confil.egg-info/PKG-INFO
+confil.egg-info/SOURCES.txt
+confil.egg-info/dependency_links.txt
+confil.egg-info/entry_points.txt
+confil.egg-info/requires.txt
+confil.egg-info/top_level.txt
+test/test_report.py
+test/test_runner.py
\ No newline at end of file
diff -r 53a61865e86e -r eaf51f9aff10 confil.egg-info/dependency_links.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confil.egg-info/dependency_links.txt	Mon Mar 04 03:28:57 2019 -0500
@@ -0,0 +1,1 @@
+
diff -r 53a61865e86e -r eaf51f9aff10 confil.egg-info/entry_points.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confil.egg-info/entry_points.txt	Mon Mar 04 03:28:57 2019 -0500
@@ -0,0 +1,3 @@
+[console_scripts]
+confil = confil.confil:confil
+
diff -r 53a61865e86e -r eaf51f9aff10 confil.egg-info/requires.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confil.egg-info/requires.txt	Mon Mar 04 03:28:57 2019 -0500
@@ -0,0 +1,1 @@
+click
diff -r 53a61865e86e -r eaf51f9aff10 confil.egg-info/top_level.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confil.egg-info/top_level.txt	Mon Mar 04 03:28:57 2019 -0500
@@ -0,0 +1,1 @@
+confil
diff -r 53a61865e86e -r eaf51f9aff10 confil.xml
--- a/confil.xml	Wed Feb 27 06:20:05 2019 -0500
+++ b/confil.xml	Mon Mar 04 03:28:57 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="confil" name="Contamination Filter (confil)" version="0.1.0">
+<tool id="confil" name="Contamination Filter (confil)" version="0.1.2">
     <requirements>
         <requirement type="package" version="7.0">click</requirement>
     </requirements>
@@ -14,7 +14,8 @@
 
         python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff 
         $input_type_conditional.single_input.element_identifier
-        && mv $report_name '$output'
+        && mv $report_name '$output_report'
+        && ln -sf "${input_type_conditional.single_input}" '$output_file1'
 
         ####### Paired Collection
         #elif $input_type == "paired_collection"
@@ -25,7 +26,9 @@
 
         python $__tool_directory__/confil/confil.py --threads $threads --cutoff $cutoff --paired 
         $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier
-        && mv $report_name '$output'
+        && mv $report_name '$output_report'
+        && ln -sf "${input_type_conditional.collection_input.forward}" '$output_file1'
+        && ln -sf "${input_type_conditional.collection_input.reverse}" '$output_file2'
         #end if
     ]]>
     </command>
@@ -46,13 +49,19 @@
         <param name="threads" type="integer" label="Number of threads" value="1" min="1" max="4" />
     </inputs>
     <outputs>
-        <data name="output" format="tabular" label="${tool.name} report" />
+        <data name="output_report" format="tabular" label="${tool.name} report" />
+        <data name="output_file1" format="fastq" label="${tool.name} report">
+        </data>
+        <data name="output_file2" format="fastq" label="${tool.name} report">
+            <filter>input_type_conditional['input_type'] == "paired_collection"</filter>
+        </data>
     </outputs>
     <tests>
         <test>
             <param name="single_input" value="seq_1.fastq" />
             <param name="input_type" value="single" />
-            <output name="output" ftype="tabular" file="seq.tab" />
+            <output name="output_report" ftype="tabular" file="seq.tab" />
+            <output name="output_file1" ftype="fastq" file="seq_1.fastq" />
         </test>
         <test>
             <param name="collection_input">
@@ -62,20 +71,13 @@
                 </collection>
             </param>
             <param name="input_type" value="paired_collection" />
-            <output name="output" ftype='tabular' file="seq.tab" />
+            <output name="output_report" ftype='tabular' file="seq.tab" />
+            <output name="output_file1" ftype='fastq' file="seq_1.fastq" />
+            <output name="output_file2" ftype='fastq' file="seq_2.fastq" />
         </test>
     </tests>
     <help><![CDATA[
-        Usage: confil [OPTIONS] SEQFILES...
-
-Options:
-  --db PATH          Name for Kraken 2 DB  [default:
-                     /tools/databases/kraken2/04092018/standard/; required]
-  --threads INTEGER  Number of threads  [default: 1]
-  --cutoff INTEGER   Percentage of fragments covered  [default: 90]
-  --paired           The filenames provided have paired-end reads
-  --help             Show this message and exit.
-
+        confil parses a kraken2 report and determines contamination based on a specified cutoff.
     ]]>    </help>
     <citations>
         <citation type="bibtex">
diff -r 53a61865e86e -r eaf51f9aff10 confil/__init__.pyc
Binary file confil/__init__.pyc has changed
diff -r 53a61865e86e -r eaf51f9aff10 confil/confil.pyc
Binary file confil/confil.pyc has changed
diff -r 53a61865e86e -r eaf51f9aff10 confil/kraken.pyc
Binary file confil/kraken.pyc has changed
diff -r 53a61865e86e -r eaf51f9aff10 confil/report.pyc
Binary file confil/report.pyc has changed
diff -r 53a61865e86e -r eaf51f9aff10 setup.py
--- a/setup.py	Wed Feb 27 06:20:05 2019 -0500
+++ b/setup.py	Mon Mar 04 03:28:57 2019 -0500
@@ -5,7 +5,7 @@
 
 setup(
     name='confil',
-    version='0.0.1',
+    version='0.1.2',
     url='https://github.com/COMBAT-TB/confil',
     description='Contamination filter',
     long_description=long_description,